processor ID: 25450 ========================================================================== |------------------------------------------------------------------| | | | *** Running a seeded analysis *** | | | |------------------------------------------------------------------| command line: /home/grobertson/Fi/Code/20090926_v1.3/Fi_v1.3/bin/fi -fseq /projects/remc_bigdata/Karsan/HS1238_kd/compare/FA/HS1238-compare-p1em6_9461-selfUnion-pm500bp-rgns.hg18.fa.3stage_dm_w4.fa -fout /projects/remc_bigdata/Karsan/HS1238_kd/compare/seed_RBPJ_MEME-m1/f/HS1238-compare-p1em6_9461-selfUnion-pm500bp-rgns.hg18.fa.3stage_dm_w4.fa.pwmCSL-MEME-m1.mx.minn500.weight0.de_novo -minN 500 -ev 5000 -pv 0.0001 -fpwm0 /home/grobertson/Fi/PWMs/CSL-MEME-m1.mx -em 80 -fEM 0.5 -posWt 0 -extTrim EXTRIM -verbose 1 -pgf 0 -fbm /home/grobertson/Fi/Code/20090926_v1.3/KmerFreq/hg18_kmer_1to9_freq.txt -bOrder 3 maximal buffer length: 15000 maximal number of sequences set: 100000 maximal number of bases per seq read: 20000 maximal number of sites in a motif: 150000 input (ChIP) sequence file: /projects/remc_bigdata/Karsan/HS1238_kd/compare/FA/HS1238-compare-p1em6_9461-selfUnion-pm500bp-rgns.hg18.fa.3stage_dm_w4.fa number of sequences in input file: 9461 average sequence length: 1071 total number of nucleotides: 10140208 max number of generations: 1 population size: 10 use a user-specified pwm as the seed /home/grobertson/Fi/PWMs/CSL-MEME-m1.mx fraction (number) input sequences subject to EM 1.00 (9461) scale factor for converting (double)pwm to (int)pwm 200 number of EM steps: 80 EM convergence criterion: 1.000000e-04 run EM on the starting pwm /home/grobertson/Fi/PWMs/CSL-MEME-m1.mx 10 times, each with a different maxp: 0.10*numSeq 0.20*numSeq 0.30*numSeq 0.40*numSeq 0.50*numSeq 0.60*numSeq 0.70*numSeq 0.80*numSeq 0.90*numSeq 1.00*numSeq no spaced dyads are generated and used. pop=10 gen=1 (no GA). motif prior probability type (see documentation): 0 pwm score p-value cutoff for declaring binding site: 1.000000e-04 Approximate the null llr log{p(s|M)/p(s|B)} score distribution using the llr scores of random/background sequences, where M is the EM-derived motif model and B is the 3-th order Markov backgroun model. The background sequences are simulated using the [a,c,g,t] frequencies in the input data. The number sets of background sequences generated: 10 pseudo count: 0.0005 minimal infomation for trimming/extending: 0.40 0.50 0.60 minimal no. sites for each motif: 500 base extension and trimming? no sliding window for comparing pwm similarity: 6 PWM similarity cutoff: 0.300 log(E-value) cutoff: 5000.00 number of adjacent bases included in binding site output: 10 job started: Sun Jul 11 20:51:38 2010 ========================================================================= GADEM cycle[ 1] generation[ 1] number of unique motif(s): 1 spacedDyad: yGTGGGAA motifConsensus: yyTGGGAG 1.00 fitness: -2981.60 GADEM cycle[ 2] generation[ 1] number of unique motif(s): 1 spacedDyad: yGTGGGAA motifConsensus: rGAGGsAG 0.70 fitness: -4389.39 GADEM cycle[ 3] generation[ 1] number of unique motif(s): 1 spacedDyad: yGTGGGAA motifConsensus: GsTGGGrk 0.80 fitness: -3792.92 GADEM cycle[ 4] generation[ 1] number of unique motif(s): 2 spacedDyad: yGTGGGAA motifConsensus: AAAkAAAA 0.90 fitness: -6139.38 spacedDyad: yGTGGGAA motifConsensus: GGAGGGGA 0.10 fitness: 954.56 GADEM cycle[ 5] generation[ 1] number of unique motif(s): 1 spacedDyad: yGTGGGAA motifConsensus: AGArGrAA 0.40 fitness: -1130.09 GADEM cycle[ 6] generation[ 1] number of unique motif(s): 1 spacedDyad: yGTGGGAA motifConsensus: AAGGrrAA 0.80 fitness: 452.87 GADEM cycle[ 7] generation[ 1] number of unique motif(s): 2 spacedDyad: yGTGGGAA motifConsensus: GCAGGArA 1.00 fitness: -711.27 spacedDyad: yGTGGGAA motifConsensus: GGArGrAA 0.10 fitness: 1335.34 GADEM cycle[ 8] generation[ 1] number of unique motif(s): 3 spacedDyad: yGTGGGAA motifConsensus: wTTAAAAA 1.00 fitness: -450.53 spacedDyad: yGTGGGAA motifConsensus: GCTGGGmC 0.10 fitness: 463.34 spacedDyad: yGTGGGAA motifConsensus: dGTGGrAA 0.20 fitness: 1281.84 GADEM cycle[ 9] generation[ 1] number of unique motif(s): 2 spacedDyad: yGTGGGAA motifConsensus: CCTGGsCw 0.60 fitness: -5323.00 spacedDyad: yGTGGGAA motifConsensus: TyTGrAAA 1.00 fitness: 493.04 GADEM cycle[ 10] generation[ 1] number of unique motif(s): 2 spacedDyad: yGTGGGAA motifConsensus: CCTGGrrA 0.40 fitness: 285.18 spacedDyad: yGTGGGAA motifConsensus: ACAGrAAA 1.00 fitness: 2180.67 GADEM cycle[ 11] generation[ 1] number of unique motif(s): 1 spacedDyad: yGTGGGAA motifConsensus: yAAGrAAA 0.80 fitness: 2060.32 GADEM cycle[ 12] generation[ 1] number of unique motif(s): 4 spacedDyad: yGTGGGAA motifConsensus: GAGkkCAG 0.50 fitness: -835.62 spacedDyad: yGTGGGAA motifConsensus: TTTTwGTA 0.70 fitness: -281.00 spacedDyad: yGTGGGAA motifConsensus: AAArwGAA 0.60 fitness: 1834.32 spacedDyad: yGTGGGAA motifConsensus: CAkGGGAA 0.40 fitness: 2135.25 GADEM cycle[ 13] generation[ 1] number of unique motif(s): 2 spacedDyad: yGTGGGAA motifConsensus: TTTGAGAC 0.10 fitness: 901.66 spacedDyad: yGTGGGAA motifConsensus: TyTGAGAA 0.40 fitness: 2008.06 GADEM cycle[ 14] generation[ 1] number of unique motif(s): 3 spacedDyad: yGTGGGAA motifConsensus: rGGCwGAG 0.70 fitness: -945.63 spacedDyad: yGTGGGAA motifConsensus: ATGrdGAA 0.30 fitness: 1117.44 spacedDyad: yGTGGGAA motifConsensus: TTTsTAAA 0.10 fitness: 1816.60 GADEM cycle[ 15] generation[ 1] number of unique motif(s): 2 spacedDyad: yGTGGGAA motifConsensus: rCAGTGAG 0.60 fitness: -738.83 spacedDyad: yGTGGGAA motifConsensus: wwTGTGAA 0.20 fitness: 2137.60 GADEM cycle[ 16] generation[ 1] number of unique motif(s): 2 spacedDyad: yGTGGGAA motifConsensus: TGkGGswG 0.40 fitness: 1391.45 spacedDyad: yGTGGGAA motifConsensus: AmAGrAAG 0.80 fitness: 1508.91 GADEM cycle[ 17] generation[ 1] number of unique motif(s): 1 spacedDyad: yGTGGGAA motifConsensus: mmTGGAAT 0.70 fitness: 1263.29 GADEM cycle[ 18] generation[ 1] number of unique motif(s): 2 spacedDyad: yGTGGGAA motifConsensus: swGsTGAG 0.20 fitness: 1617.72 spacedDyad: yGTGGGAA motifConsensus: CTGGGGAG 1.00 fitness: 2264.08 GADEM cycle[ 19] generation[ 1] number of unique motif(s): 2 spacedDyad: yGTGGGAA motifConsensus: CAAGTGAT 0.10 fitness: 1848.91 spacedDyad: yGTGGGAA motifConsensus: AAAGrsAG 0.30 fitness: 1968.41 GADEM cycle[ 20] generation[ 1] number of unique motif(s): 1 spacedDyad: yGTGGGAA motifConsensus: vATGkGAG 0.20 fitness: 1942.65 GADEM cycle[ 21] generation[ 1] number of unique motif(s): 1 spacedDyad: yGTGGGAA motifConsensus: ATTTGAAT 1.00 fitness: 1384.31 GADEM cycle[ 22] generation[ 1] number of unique motif(s): 1 spacedDyad: yGTGGGAA motifConsensus: TTTsAAAk 0.40 fitness: 1525.44 GADEM cycle[ 23] generation[ 1] number of unique motif(s): 2 spacedDyad: yGTGGGAA motifConsensus: CCTGGGkk 0.60 fitness: 882.17 spacedDyad: yGTGGGAA motifConsensus: TTTGwGwT 0.30 fitness: 2127.49 GADEM cycle[ 24] generation[ 1] number of unique motif(s): 3 spacedDyad: yGTGGGAA motifConsensus: sCwGGAAG 1.00 fitness: 1360.42 spacedDyad: yGTGGGAA motifConsensus: CTTGrAAr 0.30 fitness: 2000.97 spacedDyad: yGTGGGAA motifConsensus: AATrAAwA 0.20 fitness: 2237.48 GADEM cycle[ 25] generation[ 1] number of unique motif(s): 4 spacedDyad: yGTGGGAA motifConsensus: rGTGGswG 0.70 fitness: 1786.13 spacedDyad: yGTGGGAA motifConsensus: TCTTTGCT 0.50 fitness: 1961.07 spacedDyad: yGTGGGAA motifConsensus: AAATAAAT 0.10 fitness: 2214.68 spacedDyad: yGTGGGAA motifConsensus: TGTkTCTk 0.60 fitness: 2310.71 GADEM cycle[ 26] generation[ 1] number of unique motif(s): 3 spacedDyad: yGTGGGAA motifConsensus: CCTGwAAT 0.80 fitness: 1746.88 spacedDyad: yGTGGGAA motifConsensus: CAGGTGAw 0.20 fitness: 2384.40 spacedDyad: yGTGGGAA motifConsensus: TATAAAAT 1.00 fitness: 3024.59 GADEM cycle[ 27] generation[ 1] number of unique motif(s): 2 spacedDyad: yGTGGGAA motifConsensus: GswGGwGG 0.50 fitness: 1327.37 spacedDyad: yGTGGGAA motifConsensus: TGTGGrdT 0.20 fitness: 2028.22 GADEM cycle[ 28] generation[ 1] number of unique motif(s): 2 spacedDyad: yGTGGGAA motifConsensus: GmTGrAAA 0.20 fitness: 2031.61 spacedDyad: yGTGGGAA motifConsensus: AGAGAAAk 1.00 fitness: 2171.87 GADEM cycle[ 29] generation[ 1] number of unique motif(s): 4 spacedDyad: yGTGGGAA motifConsensus: TTTkGAAG 0.90 fitness: 708.69 spacedDyad: yGTGGGAA motifConsensus: ATTTTwAw 0.60 fitness: 1805.93 spacedDyad: yGTGGGAA motifConsensus: ATAATAAA 0.70 fitness: 2294.39 spacedDyad: yGTGGGAA motifConsensus: AGTTCAAG 0.80 fitness: 2558.60 GADEM cycle[ 30] generation[ 1] number of unique motif(s): 5 spacedDyad: yGTGGGAA motifConsensus: AkTGGAAA 0.60 fitness: 702.24 spacedDyad: yGTGGGAA motifConsensus: TGAGCCAs 1.00 fitness: 1514.50 spacedDyad: yGTGGGAA motifConsensus: ACAGGCmT 0.70 fitness: 2080.72 spacedDyad: yGTGGGAA motifConsensus: TAkrAAAA 0.10 fitness: 2443.55 spacedDyad: yGTGGGAA motifConsensus: AAwGTwAA 0.20 fitness: 2456.91 GADEM cycle[ 31] generation[ 1] number of unique motif(s): 5 spacedDyad: yGTGGGAA motifConsensus: CTGrrGCm 0.60 fitness: 1741.96 spacedDyad: yGTGGGAA motifConsensus: TATrGrAA 0.10 fitness: 2157.32 spacedDyad: yGTGGGAA motifConsensus: CTTGGsCw 0.20 fitness: 2196.04 spacedDyad: yGTGGGAA motifConsensus: TTTGGGGr 0.90 fitness: 2454.06 spacedDyad: yGTGGGAA motifConsensus: kCTCTGrG 1.00 fitness: 2514.75 GADEM cycle[ 32] generation[ 1] number of unique motif(s): 3 spacedDyad: yGTGGGAA motifConsensus: CTGGGGAr 0.40 fitness: 1944.93 spacedDyad: yGTGGGAA motifConsensus: TyTsTGAG 1.00 fitness: 2384.60 spacedDyad: yGTGGGAA motifConsensus: CTksAGAA 0.10 fitness: 2523.50 GADEM cycle[ 33] generation[ 1] number of unique motif(s): 4 spacedDyad: yGTGGGAA motifConsensus: ATTTkTwT 0.50 fitness: 1749.70 spacedDyad: yGTGGGAA motifConsensus: CTkGTGAG 0.10 fitness: 2217.11 spacedDyad: yGTGGGAA motifConsensus: TGGGTsAG 0.90 fitness: 2803.46 spacedDyad: yGTGGGAA motifConsensus: ATTTTGAT 0.20 fitness: 2836.18 GADEM cycle[ 34] generation[ 1] number of unique motif(s): 4 spacedDyad: yGTGGGAA motifConsensus: dGTGTGGT 0.80 fitness: 1773.17 spacedDyad: yGTGGGAA motifConsensus: GTTGGGrr 0.30 fitness: 2252.34 spacedDyad: yGTGGGAA motifConsensus: rTTTGGAG 0.20 fitness: 2332.74 spacedDyad: yGTGGGAA motifConsensus: AGGGkGAG 0.10 fitness: 2592.55 GADEM cycle[ 35] generation[ 1] number of unique motif(s): 3 spacedDyad: yGTGGGAA motifConsensus: TGwkTCAT 0.70 fitness: 1468.69 spacedDyad: yGTGGGAA motifConsensus: GCTGkGCT 0.20 fitness: 1941.67 spacedDyad: yGTGGGAA motifConsensus: CGGGGsCG 0.10 fitness: 2574.76 GADEM cycle[ 36] generation[ 1] number of unique motif(s): 4 spacedDyad: yGTGGGAA motifConsensus: TGwGTGAs 0.60 fitness: 1843.74 spacedDyad: yGTGGGAA motifConsensus: AAdGAGAy 0.50 fitness: 2198.58 spacedDyad: yGTGGGAA motifConsensus: TrTTTTTk 1.00 fitness: 2574.25 spacedDyad: yGTGGGAA motifConsensus: sGGGGCGG 0.10 fitness: 2782.76 GADEM cycle[ 37] generation[ 1] number of unique motif(s): 4 spacedDyad: yGTGGGAA motifConsensus: AAwGTsCT 0.40 fitness: 1387.80 spacedDyad: yGTGGGAA motifConsensus: TGTTTTww 0.90 fitness: 1633.32 spacedDyad: yGTGGGAA motifConsensus: GkGGrCAG 0.10 fitness: 1917.98 spacedDyad: yGTGGGAA motifConsensus: ACTGGGAr 0.20 fitness: 2122.77 GADEM cycle[ 38] generation[ 1] number of unique motif(s): 3 spacedDyad: yGTGGGAA motifConsensus: TGTGTATA 1.00 fitness: 1322.41 spacedDyad: yGTGGGAA motifConsensus: wGTGGAAG 0.10 fitness: 2095.69 spacedDyad: yGTGGGAA motifConsensus: wGTGTGAG 0.20 fitness: 2183.75 GADEM cycle[ 39] generation[ 1] number of unique motif(s): 1 spacedDyad: yGTGGGAA motifConsensus: CCTGGCwd 0.50 fitness: 1312.84 GADEM cycle[ 40] generation[ 1] number of unique motif(s): 2 spacedDyad: yGTGGGAA motifConsensus: CTTGGCwb 0.20 fitness: 1872.71 spacedDyad: yGTGGGAA motifConsensus: CTGGGCCy 0.70 fitness: 2398.28